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At SpongeBob's House, Patrick and SpongeBob are dancing to music. The music is shaking Squidward's house and Squidward tells them to lower the volume and accidentally swallows his Clarinet. SpongeBob comes over to Squidward's house and tries to get the clarinet out. He gets some of it out, but not all of it. The clarinet reed is still in Squidward's throat, causing Squidward to make clarinet sounds. Squidward is taken to Sandy's Treedome where Sandy tells SpongeBob about her new invention which includes the submarine that she is going to shrink, so she can remove the reed from Squidward's throat. She entrusts SpongeBob with the responsibility of guarding the submarine and SpongeBob does so by walking around, looking out for any trouble. Patrick walks by and encourages SpongeBob to guard the submarine inside the submarine.

They go in there and guard it when Patrick presses the shrink button, shrinking the submarine. Sandy comes back and notices them. She guides them to Squidward's brain. There, SpongeBob and Patrick start to hit parts of the brain, causing Squidward to lose self-control. For a moment, SpongeBob and Patrick actually fight each other for control of the vehicle and land in Squidward's stomach, where the gastric acid starts to eat the submarine away. Patrick thinks of an idea: If Squidward can drink soda, then bubbles would surround them and it would refuel the submarine. Squidward drinks soda and the plan suddenly starts to work. They travel through the throat where SpongeBob removes the clarinet reed by doing what he was born to do: dance. He returns to the submarine. Now that the job is done Squidward wants them out of his body and tells them to get out of it : Patrick mishears this and presses a grow button. Sandy, SpongeBob and Squidward say, "No!" at the same time and then we see Squidward come to work at the Krusty Krab. Mr. Krabs is startled when he sees the giant submarine in his stomach. At the end, in the submarine, Patrick complains about the submarine's toilet being clogged and Squidward gets frustrated.

This episode's title and plot spoofed the 1966 Sci-Fi film: Fantastic Voyage

Reverse whirlpool is a reference to Xiaolin Showdown

It also is similar to an attack move from Ginga Naraboshi Gen

At the beginning, SpongeBob does a moonwalk.

This is the 4th popular cartoon series (not about popularity) produced by Nickelodeon Inc to parody the film Fantastic Voyage, the first was Vantastic Voyage, an episode of The Angry Beavers, second was Tiny Timmy, an episode of The Fairly OddParents and the third was Journey to the Center of Carl, an episode of Jimmy Neutron: Boy Genius.

This episode is similar to "Sandy's Rocket", by the fact that SpongeBob and Patrick stumble into one of Sandy's complicated machines.

This is the second time SpongeBob makes Squidward swallow his clarinet. The first time was in SB-129.

This is the second time Mr. Krabs said "Neptune's Trousers". The first time was in Whale of a Birthday

Closed-captioning error: when SpongeBob and Patrick are dancing at the beginning, SpongeBob says, "Tropical breeze!" However, the captions said "Tropical waves" instead.

This is probably the episode where Patrick is most stupid for many reasons: 1. Shrinking the sub after SpongeBob says he had to guard it. 2. Destroying the air tanks/controls. 3. Pressing the GROW button when Squidward said Go. And 4. telling Squidward about the submarine's toilet being back up

This marks the first time that Squidward is in Sandy's treedome.

When SpongeBob and Squidward are in Sandy's treedome, the bowls on their heads have the opening oriented up, like in Tea at the Treedome and Chimps Ahoy.

The title card BG is like the part when SpongeBob and Patrick enter Squidward's brain except without the sub.